臺灣博碩士論文加值系統

雖然目前一般認為新鼠海豚屬(Neophocaena)為一包含三個亞種的單種屬，但新鼠海豚屬內的分類仍存在一些爭議。江豚(“Neophocaena phocaenoides”)是嚴重遭受人類活動干擾的小型鯨類，目前被列入華盛頓公約的「附錄一」中。談到保育，最首要的是要有明確的「保育單元(units)」。存在東海南端(包括台灣海峽)的江豚，其分類地位在過去型態研究上呈現爭議的現象。本研究，根據4個微衛星體的分析，認為此地區的江豚應屬於”北方亞種”。本研究比較了夏等人的研究中關於”長江亞種”的基因型(genotype)數據，有三群非常相異的基因群存在新鼠海豚屬，此三群分別是:（1）存在南中國海及台灣海峽的W-type群，依據背脊型態特徵被認為是”指名亞種(N. p. phocaenoides)”；（2）存在長江中下游的VN-type群，認為是”長江亞種(N. p. asiaeorientalis)”；（3）存在黃海、東海、台灣海峽及南中國海北端的IN-type + UN-type 群，認為是”北方亞種(N. p. sunameri)”。根據11個微衛星體的分析， IN-type + UN-type 群和W-type群皆無群內分化的現象。W-type 群和 IN-type + UN-type 群在馬祖地區有部分共域的現象，這是一個研究其分類地位的機會。由於發現在馬祖地區的W-type 群和 UN-type 群，在型態上並沒有中間型的個體存在，且在11個微衛星體基因座的分析顯示，兩群之間也沒有雜交的個體。根據E.O.Wiley 的定義，認為W-type 群和 IN-type + UN-type 群應該是兩個種的分類地位。此外，依據Crandall 等人對演化顯著單元 (ESU)的定義，本篇研究認為在新鼠海豚屬內應該存在三個演化顯著單元（ESUs）。

Although the Neophocaena is currently thought to be monotypic (“Neophocaena phocaenoides”) with three “subspecies”, the taxonomy of this genus still remains uncertainty. The finless porpoise (“Neophocaena phocaenoides”) is one of the small cetacean species under threats from human activities. At present, finless porpoise is listed in Appendix I of Convention on International Trade in Endangered Species of Wild Flora and Fauna (CITES). For conservation issue, it is important to define appropriate and unambiguous “units”. In this study, I intended to settle the taxonomic status of the specimens of finless porpoise from the southern part of the East China Sea (including the Taiwan Strait) in which the status has been under debate. Results from this study, indicated that they should belong to “N. p. sunameri”. Comparing the genotypes of the microsatellite of additional individuals of the “N. p. asiaeorientalis” belonging to the VN-type group given in Xia and coworkers report with our data, three distinguished genetic groups were revealed: (1) the group occurring in the Taiwan Strait (i.e., the W-type group, currently recognized as “N. p. phocaenoides”); (2) the group occurred in the Yangtze Rive (i.e., the VN-type group, currently recognized as “N. p. asiaeorientalis”); (3) the group occurred in the Yellow Sea and the Taiwan strait (i.e., the IN-type + UN-type group, currently recognized as “N. p. sunameri”). Population differentiation was absent not only within the W-type group but also within the IN-type +UN-type group. I tried to detect the taxonomy of the two parapatric groups in where the W-type and IN-type +UN-type groups are co-exit sympatrically. No specimens with intermediate character state of the width of the dorsal denticles (i. e., hybrids) were presented in Matsu Islands on the Chinese coast where the W-type and UN-type groups were sympatric. Hybrid individual exhibiting the hybrid states of the 11 microsatellite loci between these two groups was also not found. According to E.O. Wiley’s criteria for recognizing species, these two groups are eligible to be considered separate species. Based on Crandall and his coworkers’ criteria of evolutionarily significant unit (ESU), the three groups, the W-type, IN-type +UN-type and VN-type groups, should be treated as three distinct ESUs.

Table of contents
Acknowledgements .……….………….……….……….……….……………..….…..i
Abstract in Chinese .……….………….……….……….……….……………..….…..iii
Abstract…….……….……….………. …….………….….……….…………………iv
Table of Contents ……….………..………….……….……….…………………….. vi
Table legends .….…………….………….……….……….…………………….... .…vii
Figure legends .…………….……….……….……….………………………………viii
Table of appendix………….……….……….……….…………………………………ix
Introduction…….……….……….…….…….…….……….……….…………………1
Materials and methods…….……….……….……….………..……….………………7
Results……….……….……….…………….……….……….……………………....13
Discussion……….…….…………….……….……….……….………………..……18
References……….……….…………….……….……….……….…………..………26

Table legends
Table 1. Primers and core sequences of the seven microsatellite loci developed from finless porpoise (Neophocaena phocaenoides) ……….……….….………….…31
Table 2. Estimates of the number of alleles per locus (A), allelic richness (AR), observed heterozygosity (HO), expected heterozygosity (HE), and Hardy-Weinberg exact test (HW) for 4 microsatellite loci in the IN-type +UN-type group, W-type group, and VN-type group of finless porpoise ……….……….……………. .….…. .32
Table 3. Estimates of the number of alleles per locus (A), allelic richness (AR), observed heterozygosity (HO), expected heterozygosity (HE), and Hardy-Weinberg exact test (HW) for 11 microsatellite loci in the IN-type +UN-type group, and W-type group of finless porpoise ……….……….……………………….…. .…. .….….33
Table 4. Pairwise estimates of Fst (Wright 1987; below diagonal) and Rst (Slatkin 1995; above diagonal) for the IN-type +UN-type group, the W-type group and the VN-type group using 4 microsatellite loci………….………………….. .…. .….34
Table 5. Estimate of the number of migrants per generation (Nm) among the IN-type +UN-type group, the W-type group and the VN-type group of finless porpoise ….……….…………………………………………….…….... .…. .…35
Table 6. Estimate of the number of female migrants per generation (Nefmf) among the IN-type +UN-type group, the W-type group and the VN-type group of finless porpoise. (modified from Yang et al. 2002 )……….…. .…. ………..….…. .….36
Table 7. Evolutionarily significant units (ESUs) of the finless porpoise were defined on the basis of genetic and ecological exchangeability. ..….…………. ….………. 37

Figure legends
Figure 1. Distribution of sample collection.…….………………….………..……….…38
Figure 2. Subdivision of groups of Neophocaena species from the Yangtze River and the western Pacific coastal waters.…….……….……….……….……..……………39
Figure 3.Subdivision of groups within the same dorsal-ridge form of finless porpoise ...40
Figure 4 Allele frequencies and size distributions of 4 microsatellite loci in the W-type, IN-type + UN-type and VN-type groups of finless porpoises.…….…….………41
Figure 5. Allele frequency distributions of 11 microsatellite loci.…………….……... ...42
Figure 6. Number of monthly samples of the W-type and UN-type groups of finless porpoises in Matsu Islands from 1994 to 2006…….……….………….…..……44
Figure 7. Number of monthly samples of the W-type and UN-type groups of finless porpoises in Fujian, China from 1994 to 1996 and 1999 …….………...……….45

Table of appendix
Appendix 1. Primers and core sequences of the seven microsatellite loci developed from other cetacean species……………………………………..…………………46
Appendix 2. Categories of population distinctiveness based on rejection (+) or failure to reject (-) the null hypotheses (HO) of genetic and ecological exchangeability, for both recent and historical timeframes……………………………………47
Appendix 3. Typical chromatogram for 11 microsatellite loci. …….…….………..……48
Appendix 4. Genotypes of the 22 Yangtze finless porpoise (the VN-type group) given by Xia et al. (2005) ..……………………………………………………...….…50

Amano, M., N. Miyazaki, and K. Kureha. 1992. A morphological comparison of skulls of the finless porpoise Neophocaena phocaenoides from the Indian Ocean, Yangtze River and Japanese waters. Journal of the Mammalogical Society of Japan 17:59–69.
Amano, M., F. Nakahara, A. Hayano, and K. Shirakihara. 2003. Abundance estimate of finless porpoises off the Pacific coast of eastern Japan based on aerial surveys. Mammal Study 28:103-110.
Beaumont, M. and M. Bruford. 1999. Microsatellites in conservation genetics. In: Microsatellite: Evolution and Application. (eds. Goldstein DB, Schlötterer C). Oxford University Press, New York. .
Berube, M., H. Jorgensen, R. McEwing, and P. J. Palsboll. 2000. Polymorphic di-nucleotide microsatellite loci isolated from the humpback whale, Megaptera novaeangliae. Molecular Ecology 9:2181-3.
Crandall, K. A., O. R. R. Bininda-Emonds, G. M. Mace, and R. K. Wayne. 2000. Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution 15:290-295.
DeWoody, J. A., and J. C. Avise. 2000. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. Journal of Fish Biology 56:461-473.
Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. . Evolutionary Bioinformatics Online 1:47-50.
Gaggiotti, O. E., O. Lange, K. Rassmann, and C. Gliddon. 1999. A comparison of two indirect methods for estimating average levels of gene flow using microsatellite data. Molecular Ecology 8:1513-1520.
Gao, A., and K. Zhou. 1993. Growth and reproduction of three populations of finless porpoise, Neophocaena phocaenoides, in Chinese waters. Aquatic mammal 19:3-12.
Gao, A., and K. Zhou. 1995a. Geographical variation of external measurements and three subspecies of Neophocaena phocaenoides in Chinese waters. Acta Theriologica Sinica 15(2):81-92.
Gao, A., and K. Zhou. 1995b. Geographical variations of postcranial skeleton among the populations of Neophocaena in Chinese waters. Acta Theriologica Sinica 15 (4):246-253.
Gao, A., and K. Zhou. 1995c. Geographical variations of skull among the populations of Neophocaena in Chinese waters. Acta Theriologica Sinica 15:161-169.
Gemmell, N. J., and S. Akiyama. 1996. An efficient method for the extraction of DNA from vertebrate tissues. Trends in Genetics 12:338-339
Goodman, S. J. 1997. R(st) calc: A collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Molecular Ecology 6:881-885.
Goudet, J. FSTAT, a Program to Estimate and Test Gene Diversities and Fixation Indices (Version 2.9.3).
Goudet, J. 1995. FSTAT (Version 1.2): A computer program to calculate F-statistics. Journal of Heredity 86:485-486.
Guo, S. W., and E. A. Thompson. 1992. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48:359.
Hamilton, M. B., E. L. Pincus, A. Di Fiore, and R. C. Fleischer. 1999. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques 27:500-507.
Huang, Z., W. Liu, C. Zheng, and C. Li. 2000. Finless porpoises (Neophocaena phocaenoides) in the southern coastal waters of Fujian, China. Acta Oceanologica Sinica 22:100-105.
IWC 2001. Annex K. Report of the standing sub-committee on small cetaceans. Journal of Cetacean Research and Management 5(Supplement):263-291.
Jarne, P., and P. J. L. Lagoda. 1996. Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution 11:424-429.
Jefferson, T. A. 2002. Preliminary analysis of geographic variation in cranial morphometrics of the finless porpoise (Neophocaena phocaenoides). Raffles Bulletin of Zoology (SUPPL. 10):3-14.
Jefferson, T. A., and S. K. Hung. 2005. Overview of the biology and status of the finless porpoise Neophocaena phocaenoides. IWC Scientific Committee Meeting, Ulsan, Korea SC/57/SM1.
Kasuya, T. 1999. Finless porpoise Neophocaena phocaenoides (G. Cuvier, 1829). Handbook of Marine Mammals, Vol. 6: The Second Book of Dolphins and the Porpoises 6:411-442.
Marshall, T. C., J. Slate, L. E. B. Kruuk, and J. M. Pemberton. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7:639-655.
Moritz, C. 1994. Defining ''evolutionarily significant units'' for conservation. Trends in Ecology and Evolution 9:373-375.
Pichler, F. B., and C. S. Baker. 2000. Loss of genetic diversity in the endemic Hector''s dolphin due to fisheries-related mortality. Proceedings of the Royal Society - Biological Sciences (Series B) 267:97-102.
Pilleri, G., and P. Chen. 1980. Neophocaena phocaenoides and Neophocaena asiaeorientalis: taxonomical differences. Investigations on Cetacea 11:25-32.
Pilleri, G., and M. Gihr. 1975. On the taxonomy and ecology of the finless black porpoise, Neophocaena (Cetacea, Delphinidae). Mammalia 39:657-73.
Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
Raymond, M., and F. Rousset. 1995. GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. Journal of Heredity 86:248-249.
Reeves, R. R., J. Y. Wang, and S. Leatherwood. 1997. The finless porpoise, Neophocaena phocaenoides (G. Cuvier 1829): A summary of current knowledge and recommendations for conservation action. Asian Marine Biology 14:111-143.
Rice, D. W. 1998. Marine Mammals of the World: Systematics and Distribution.
Rooney, A. P., D. B. Merritt, and J. N. Derr. 1999. Microsatellite diversity in captive bottlenose dolphins (Tursiops truncatus). The Journal of Heredity 90:228-31.
Rosel, P. E., S. C. France, J. Y. Wang, and T. D. Kocher. 1999. Genetic structure of harbour porpoise Phocoena phocoena populations in the northwest Atlantic based on mitochondrial and nuclear markers. Molecular Ecology 8 (12 SUPPL. 1).
Ryder, O. A. 1986. Species conservation and systematics: The dilemma of subspecies. Trends in Ecology and Evolution 1:9-10.
Shirakihara, M., K. Shirakihara, and A. Takemura. 1994. Distribution and seasonal density of the finless porpoise Neophocaena phocaenoides in the coastal waters of western Kyushu, Japan. Fish. Sci. 60:41-46.
Slatkin, M. 1991. Inbreeding coefficients and coalescence times. Genetical Research 58:167-175.
Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457-462.
Valsecchi, E., and W. Amos. 1996. Microsatellite markers for the study of cetacean populations. Molecular Ecology 5:151-156.
Van Bree, P. J. H. 1973. Neophocaena phocaenoides asiaeorientalis (Pilleri and Gihr, 1973), a synonym of the preoccupied name Delphinus melas Schlegel, 1841. Beaufortia 24(17-24).
Wang, P. 1992. On the taxonomy of the finless porpoise in China. Fisheries Science 11:10–14.
Wang, P. 1999. Chinese cetaceans. Ocean Enterprises Ltd, Hong Kong.
Wiley, E. O. 1981. Phylogenetics. The Theory and Practice of Phylogenetic Systematics. Wiley-Interscience, New York.
Wright, S. 1969. Evolution and the Genetics of Populations: Volume 2. The Theory of Gene Frequencies, University of Chicago Press, Chicago.
Xia, J.-H., J.-S. Zheng, and W. Ding. 2005. Individual identification of the Yangtze finless porpoises Neophocaena phocaenoides asiaeorientalis inhabiting the Tian-e-Zhou Natural Reserve based on microsatellite fingerprint. Acta Zoologica Sinica 51:142-148.
Xiao, W., and X. Zhang. 2002. Distribution and population size of Yangtze finless porpoise in Poyang Lake and its branches. Acta Theriologica Sinica 22:7-14.
Yamada, T. K., and M. Okamoto. 2000. Distribution survey of finless porpoise in the Inland of Japan. Memoirs of the National Science Museum , Tokyo 32:157-165.
Yang, G., W. Ren, K. Zhou, S. Liu, G. Ji, J. Yan, and L. Wang. 2002. Population genetic structure of finless porpoises, Neophocaena phocaenoides, in Chinese waters, inferred from mitochondrial control region sequences. Marine Mammal Science 18:336-347.
Yoshida, H., K. Shirakihara, H. Kishino, M. Shirakihara, and A. Takemura. 1998. Finless porpoise abundance in Omura Bay, Japan: Estimation from aerial sighting surveys. Journal of Wildlife Management 62:286-291.
Yoshida, H., M. Yoshioka, M. Shirakihara, and S. Chow. 2001. Population structure of finless porpoises (Neophocaena phocaenoides) in coastal waters of Japan based on mitochondrial DNA sequences. Journal of Mammalogy 82:123-130.
Zhang, X., R. Liu, Q. Zhao, G. Zhang, Z. Wei, X. Wang, and J. Yang. 1993. The population of finless porpoise in the middle and lower reaches of Yangtze River. Acta Theriologica Sinica 13:260-270.
Zheng, J. S., J. H. Xia, S. P. He, and D. Wang. 2005. Population genetic structure of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis): implications for management and conservation. Biochem Genet 43:307-20.